Le Roux gave his daughters several short-term contracts between 2009 and 2016 for which they earned a total of 55,000 euros ($59,500).
Le Roux, 51, was to meet Socialist Prime Minister Bernard Cazeneuve later in the day to provide explanations over the latest scandal to hit France's already embattled political class with elections a month away.
The TMC channel reported late Monday that Le Roux gave his daughters several short-term contracts between 2009 and 2016 for which they earned a total of 55,000 euros ($59,500).
The girls were still in school when he first hired them and continued doing work for him -- paid with taxpayers' money -- when they were in university.
Le Roux, who has denied any wrongdoing, told TMC his daughters had worked for him during their summer holidays.
He has only held the interior portfolio since December after taking over from Cazeneuve, and faced his most serious crisis at the weekend when a man was shot dead at Paris's Orly airport after attacking a soldier.
Cazeneuve, without naming Le Roux or referring to the scandal, said at a Paris event on Tuesday that government officials must be "irreproachable".
"Otherwise the authority of the state is weakened," Cazeneuve said.
Le Roux was conspicuously absent from the event after initially being scheduled to attend.
The interior minister also slipped out of a Senate hearing without speaking to reporters and cancelled two other appearances on Tuesday.
French lawmakers are allowed to hire family members as assistants, as long as they do real work.
Fillon, once the frontrunner in France's presidential race, has been charged with misuse of public funds after placing his wife Penelope and two of their children on the public payroll.
In the scandal dubbed "Penelopegate", they are suspected of holding fake jobs as parliamentary aides for which they were paid around 900,000 euros.
The conservative presidential candidate also insists he did no wrong, presenting the affair as an attempted "political assassination" and questioning the justice system's impartiality.
In a clear reference to Fillon, Cazeneuve said Tuesday that public figures should not challenge the independence of the judiciary.
The expenses scandal, and later revelations about lavish gifts from the rich, have dealt a severe blow to Fillon's campaign.
The former prime minister sought to shift the focus to his cost-cutting platform in a debate on Monday among the top five presidential candidates.
With one month to go before the first round of elections for a successor to the deeply unpopular Socialist President Francois Hollande -- who decided in December not to seek re-election -- the electorate is especially disillusioned.
Only 17 percent of those questioned in an Ipsos poll last month gave high marks to France's democratic system.